Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 20 of 221
Found at i:5740525 original size:11 final size:11
Alignment explanation
Indices: 5740509--5740536 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5740499 GTTGTTACAG
5740509 GAAAATATGTT
1 GAAAATATGTT
5740520 GAAAATATGTT
1 GAAAATATGTT
5740531 GAAAAT
1 GAAAAT
5740537 TTGGGTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (11 bp):
GAAAATATGTT
Found at i:5741625 original size:26 final size:27
Alignment explanation
Indices: 5741596--5741651 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
5741586 AAATCACAGA
* * *
5741596 CCCAAAATCT-AACCCAATTAGCTTAG
1 CCCAAAACCTAAACCCAATTAACCTAG
5741622 CCC-AAACCTAAACCCAATTAACCTAG
1 CCCAAAACCTAAACCCAATTAACCTAG
5741648 CCCA
1 CCCA
5741652 GCTAATGTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.39, C:0.38, G:0.05, T:0.18
Consensus pattern (27 bp):
CCCAAAACCTAAACCCAATTAACCTAG
Found at i:5745465 original size:18 final size:18
Alignment explanation
Indices: 5745444--5745504 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
5745434 ATTCATATGT
*
5745444 ATTTTATAGTATATATAC
1 ATTTTATAATATATATAC
* *
5745462 ATTTCATAATATTTATAC
1 ATTTTATAATATATATAC
*
5745480 ATTTTCTATAATATACATAC
1 A-TTT-TATAATATATATAC
5745500 ATTTT
1 ATTTT
5745505 TATATCTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 17 0.49
19 6 0.17
20 12 0.34
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.51
Consensus pattern (18 bp):
ATTTTATAATATATATAC
Found at i:5745490 original size:20 final size:20
Alignment explanation
Indices: 5745448--5745508 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
5745438 ATATGTATTT
*
5745448 TATAGTATATATACA-TTTC
1 TATAATATATATACATTTTC
*
5745467 -ATAATATTTATACATTTTC
1 TATAATATATATACATTTTC
*
5745486 TATAATATACATACATTTT-
1 TATAATATATATACATTTTC
5745505 TATA
1 TATA
5745509 TCTTTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 12 0.33
19 8 0.22
20 16 0.44
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (20 bp):
TATAATATATATACATTTTC
Found at i:5745901 original size:17 final size:17
Alignment explanation
Indices: 5745879--5745912 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5745869 TGGGATTTTC
5745879 GAGGAAATTGAGCCCTA
1 GAGGAAATTGAGCCCTA
5745896 GAGGAAATTGAGCCCTA
1 GAGGAAATTGAGCCCTA
5745913 ACGTATTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (17 bp):
GAGGAAATTGAGCCCTA
Found at i:5751263 original size:44 final size:44
Alignment explanation
Indices: 5751215--5751397 Score: 107
Period size: 44 Copynumber: 4.2 Consensus size: 44
5751205 TTAGATCTTG
*
5751215 CCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTA
1 CCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGGCGGATTTTA
** * * * * *** ** *
5751259 CCTCCCTAAAGTTGCAGTGTAGTACATTGAAGCCAG-TAATTCTA
1 CCTCCCT-AAGCAGCAGTGGAGCAGATCGAAGATGGCGGATTTTA
* * ** * ** * ** * * *
5751303 CTTCCTTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTG
1 CCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGGCGGATTTTA
*
5751347 CCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTA
1 CCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGGCGGATTTTA
5751391 CCTCCCT
1 CCTCCCT
5751398 GAAGTTGCAG
Statistics
Matches: 91, Mismatches: 46, Indels: 4
0.65 0.33 0.03
Matches are distributed among these distances:
43 16 0.18
44 57 0.63
45 18 0.20
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (44 bp):
CCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGGCGGATTTTA
Found at i:5751333 original size:132 final size:132
Alignment explanation
Indices: 5751096--5751821 Score: 1076
Period size: 132 Copynumber: 5.5 Consensus size: 132
5751086 CCTGCATCGA
* * * * **
5751096 TAGTGGAGCAGGTCAAAGATGACAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCC
1 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCC
* *
5751161 AGTAATTCTACTTCCCTGGTCAGCAGTGGAATAGATTGAAGATTTTAGATCTTGCCTCCCTAAGC
66 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGC
5751226 AG
131 AG
* * *
5751228 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTAAAGTTGCAGTGTAGTACATTGAAGCC
1 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCC
* *
5751293 AGTAATTCTACTTCCTTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGC
66 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGC
5751358 AG
131 AG
* *
5751360 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTAGAGTACATTGAAGCC
1 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCC
* * *
5751425 AGTAATTCTACTTTCCTGGGTAGCAGCGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGC
66 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGC
5751490 AG
131 AG
* *
5751492 TAGTGGAGCAGATCGAAGATGGCGAATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCC
1 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCC
* *
5751557 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCTTAAGC
66 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGC
5751622 AG
131 AG
* * * * ** *
5751624 TAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCTTGTGGTTACAGTGGAGTACATTAAAGCC
1 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCC
* * * * * *
5751689 AATAATTCTACTTCCCTGGGTAGCAGTGGAATAGTTTGAAGATTTCATATATTGTCTCCCTAAGC
66 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGC
5751754 AG
131 AG
* * * * *
5751756 TAGTAGAGTAGA-CTGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAATAGATTGAAGC
1 TAGTGGAGCAGATC-GAAGATGGCGGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGC
5751820 CA
65 CA
5751822 CCAATCCTAT
Statistics
Matches: 544, Mismatches: 49, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
131 1 0.00
132 543 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (132 bp):
TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCC
AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGCCTCCCTAAGC
AG
Found at i:5752509 original size:18 final size:18
Alignment explanation
Indices: 5752479--5752513 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5752469 CCTAGGAAGG
5752479 ATTTTCTTTTTTCTTTTT
1 ATTTTCTTTTTTCTTTTT
5752497 ATTTT-TTTATTTCTTTT
1 ATTTTCTTT-TTTCTTTT
5752514 CGGATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (18 bp):
ATTTTCTTTTTTCTTTTT
Found at i:5753256 original size:18 final size:18
Alignment explanation
Indices: 5753235--5753295 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
5753225 ATTCATATGT
*
5753235 ATTTTATAGTATATATAC
1 ATTTTATAATATATATAC
* *
5753253 ATTTCATAATATTTATAC
1 ATTTTATAATATATATAC
*
5753271 ATTTTCTATAATATACATAC
1 A-TTT-TATAATATATATAC
5753291 ATTTT
1 ATTTT
5753296 TATATCTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 17 0.49
19 6 0.17
20 12 0.34
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.51
Consensus pattern (18 bp):
ATTTTATAATATATATAC
Found at i:5753281 original size:20 final size:20
Alignment explanation
Indices: 5753239--5753299 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
5753229 ATATGTATTT
*
5753239 TATAGTATATATACA-TTTC
1 TATAATATATATACATTTTC
*
5753258 -ATAATATTTATACATTTTC
1 TATAATATATATACATTTTC
*
5753277 TATAATATACATACATTTT-
1 TATAATATATATACATTTTC
5753296 TATA
1 TATA
5753300 TCTTTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 12 0.33
19 8 0.22
20 16 0.44
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (20 bp):
TATAATATATATACATTTTC
Found at i:5753688 original size:17 final size:17
Alignment explanation
Indices: 5753666--5753699 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5753656 TGGGATTTTC
5753666 GAGGAAATTGAGCCCTA
1 GAGGAAATTGAGCCCTA
5753683 GAGGAAATTGAGCCCTA
1 GAGGAAATTGAGCCCTA
5753700 ACGTATTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (17 bp):
GAGGAAATTGAGCCCTA
Found at i:5754722 original size:18 final size:18
Alignment explanation
Indices: 5754664--5754724 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
5754654 TATTTTAAAT
5754664 TTTTAAATATTTATAAAAA
1 TTTTAAA-ATTTATAAAAA
** ***
5754683 TTCCAAAATTTATAATTT
1 TTTTAAAATTTATAAAAA
*
5754701 TTTTAAAAATTATAAAAA
1 TTTTAAAATTTATAAAAA
5754719 TTTTAA
1 TTTTAA
5754725 TTAATTAATT
Statistics
Matches: 31, Mismatches: 11, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
18 26 0.84
19 5 0.16
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTTAAAATTTATAAAAA
Found at i:5755395 original size:16 final size:17
Alignment explanation
Indices: 5755374--5755414 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
5755364 TAAATATGTT
*
5755374 ATTTTTAG-GTTTTATA
1 ATTTTTAGAGTTTTAAA
5755390 ATTTTT-GAGTTTTAAA
1 ATTTTTAGAGTTTTAAA
5755406 ATTTTTAGA
1 ATTTTTAGA
5755415 TTCGGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 19 0.86
17 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (17 bp):
ATTTTTAGAGTTTTAAA
Found at i:5758059 original size:18 final size:19
Alignment explanation
Indices: 5758036--5758077 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
5758026 GAAGTTTTCT
5758036 ATTATTGTAATAT-TGTTA
1 ATTATTGTAATATATGTTA
* *
5758054 ATTATTTTAATATATTTTA
1 ATTATTGTAATATATGTTA
5758073 ATTAT
1 ATTAT
5758078 ATATTAACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTATTGTAATATATGTTA
Found at i:5758063 original size:9 final size:9
Alignment explanation
Indices: 5758036--5758077 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
5758026 GAAGTTTTCT
*
5758036 ATTATTGTA
1 ATTATTTTA
5758045 A-TATTGTTA
1 ATTATT-TTA
5758054 ATTATTTTA
1 ATTATTTTA
5758063 ATATATTTTA
1 AT-TATTTTA
5758073 ATTAT
1 ATTAT
5758078 ATATTAACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
8 4 0.14
9 12 0.41
10 13 0.45
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (9 bp):
ATTATTTTA
Found at i:5759279 original size:27 final size:27
Alignment explanation
Indices: 5759236--5759307 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
5759226 TTTTGGTTTC
5759236 TTCGAGGTTC-AGTGTTTGGTGTTCATGG
1 TTCGAGGTTCGAG-GTTTGG-GTTCATGG
5759264 TTCGA-GTTCGAGGTTTAGGGTTCATGG
1 TTCGAGGTTCGAGGTTT-GGGTTCATGG
*
5759291 TTCAAGGTTCG-GGTTTG
1 TTCGAGGTTCGAGGTTTG
5759308 AGATTCGAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
26 1 0.03
27 25 0.62
28 14 0.35
ACGTcount: A:0.12, C:0.11, G:0.36, T:0.40
Consensus pattern (27 bp):
TTCGAGGTTCGAGGTTTGGGTTCATGG
Found at i:5759431 original size:21 final size:20
Alignment explanation
Indices: 5759370--5759445 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 20
5759360 TCAAGGTTTT
* *
5759370 GGTTTTGGGTTCGAGGTTCGA
1 GGTTTAGGGTTCGA-GTTCAA
*
5759391 TGTTTAGGGTTCGAGTTCAA
1 GGTTTAGGGTTCGAGTTCAA
5759411 GGTTTAGGGTTCTTG-GTTCAA
1 GGTTTAGGGTTC--GAGTTCAA
*
5759432 GGTTT-GGCTTCGAG
1 GGTTTAGGGTTCGAG
5759446 ATTTGGGTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 21 0.45
21 23 0.49
22 1 0.02
ACGTcount: A:0.13, C:0.11, G:0.37, T:0.39
Consensus pattern (20 bp):
GGTTTAGGGTTCGAGTTCAA
Found at i:5761243 original size:16 final size:17
Alignment explanation
Indices: 5761200--5761245 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
5761190 AAATATATAT
*
5761200 TTTTATAATTTTCAATAA
1 TTTTA-AATTTTTAATAA
5761218 TTTT-AA-TTTTAA-AA
1 TTTTAAATTTTTAATAA
5761232 TTTTAAATTTTTAA
1 TTTTAAATTTTTAA
5761246 CAAATTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 6 0.24
15 7 0.28
16 8 0.32
18 4 0.16
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTAAATTTTTAATAA
Found at i:5767767 original size:19 final size:19
Alignment explanation
Indices: 5767743--5767783 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
5767733 ACGATATAGG
5767743 ATGGATACCTAGAATGCAA
1 ATGGATACCTAGAATGCAA
5767762 ATGGATACCTAGAATGCAA
1 ATGGATACCTAGAATGCAA
5767781 ATG
1 ATG
5767784 CATTCTAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (19 bp):
ATGGATACCTAGAATGCAA
Found at i:5767864 original size:6 final size:6
Alignment explanation
Indices: 5767855--5767883 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5767845 AAGATCAAGA
5767855 TGGAGG TGGAGG TGGAGG TGGAGG TGGAG
1 TGGAGG TGGAGG TGGAGG TGGAGG TGGAG
5767884 ATAGGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.66, T:0.17
Consensus pattern (6 bp):
TGGAGG
Found at i:5772473 original size:21 final size:20
Alignment explanation
Indices: 5772435--5772474 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5772425 TTTCATTTAC
*
5772435 CTTTTTTTCTTCTTCTTTTT
1 CTTTTTTTCTTCTCCTTTTT
*
5772455 CTTTTCTTTGTTCTCCTTTT
1 CTTTT-TTTCTTCTCCTTTT
5772475 AATTCTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.75
Consensus pattern (20 bp):
CTTTTTTTCTTCTCCTTTTT
Found at i:5783183 original size:88 final size:88
Alignment explanation
Indices: 5783002--5783656 Score: 1046
Period size: 88 Copynumber: 7.5 Consensus size: 88
5782992 AACAGATCAG
** * * * * * *
5783002 TGAAGACAGCAGATCTTGCCTTCCCGCGTTAACAGCGAAGTAGATCGAAAACA-AAACCTTGCCT
1 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTTCCT
* *
5783066 CTCTCGGTGGTAATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * * *
5783089 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAAACACAAACCTTTCCT
1 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTTCCT
5783154 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
5783177 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTTCCT
1 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTTCCT
5783242 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
5783265 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTTCCT
1 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTTCCT
5783330 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
5783353 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTTCCT
1 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTTCCT
5783418 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
5783441 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTTCCT
1 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTTCCT
5783506 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* ** * * * *
5783529 TGAAGACAAAAGATCTTGCCTTCCTATATTGATAGCGAAGCAGGTCCAAGACACAAACC-TTGC-
1 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTTCCT
*
5783592 CTCTCGGTGGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * * * *
5783615 TGAAGACAAAAGATTTTGCCTTCCTGTAATGACAGCGGAGCA
1 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCA
5783657 AACTAAAGAT
Statistics
Matches: 539, Mismatches: 28, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
86 59 0.11
87 48 0.09
88 432 0.80
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.25
Consensus pattern (88 bp):
TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTTCCT
CTCTCGGTTGTGATGGAGCTGGT
Found at i:5783808 original size:44 final size:44
Alignment explanation
Indices: 5783002--5783818 Score: 179
Period size: 44 Copynumber: 18.6 Consensus size: 44
5782992 AACAGATCAG
* * * *
5783002 TGAAGACAGCAGATCTTGCCT-TCCCGCGTTAACAGCGAAGTAGAT
1 TGAAGACA-CAAATCTTGCCTCTCTCGC-TTGACAGCGAAGCAGAT
* * * * * * *
5783047 CGAAAACA-AAACCTTGCCTCTCTCGGTGGTA-ATG-G-AGCTGGT
1 TGAAGACACAAATCTTGCCTCTCTCGCTTG-ACA-GCGAAGCAGAT
* * *
5783089 TGAAGACAAAAGATCTTGCCT-TC-CTGTATTGACAGCGAAGCAGGT
1 TGAAGACACAA-ATCTTGCCTCTCTC-G-CTTGACAGCGAAGCAGAT
* * * * * ** * *
5783134 CGAAAACACAAACCTTTCCTCTCTCGGTTGTGATG-G-AGCTGGT
1 TGAAGACACAAATCTTGCCTCTCTCGCTTGACA-GCGAAGCAGAT
5783177 TGAAGACA-ATAGATCTTGCCT-TC-CTGCATTGACAGCGAAGCAGAT
1 TGAAGACACA-A-ATCTTGCCTCTCTC-GC-TTGACAGCGAAGCAGAT
* * * * ** * *
5783222 CGAAGACACAAACCTTTCCTCTCTCGGTTGTGATG-G-AGCTGGT
1 TGAAGACACAAATCTTGCCTCTCTCGCTTGACA-GCGAAGCAGAT
5783265 TGAAGACA-ATAGATCTTGCCT-TC-CTGCATTGACAGCGAAGCAGAT
1 TGAAGACACA-A-ATCTTGCCTCTCTC-GC-TTGACAGCGAAGCAGAT
* * * * ** * *
5783310 CGAAGACACAAACCTTTCCTCTCTCGGTTGTGATG-G-AGCTGGT
1 TGAAGACACAAATCTTGCCTCTCTCGCTTGACA-GCGAAGCAGAT
5783353 TGAAGACA-ATAGATCTTGCCT-TC-CTGCATTGACAGCGAAGCAGAT
1 TGAAGACACA-A-ATCTTGCCTCTCTC-GC-TTGACAGCGAAGCAGAT
* * * * ** * *
5783398 CGAAGACACAAACCTTTCCTCTCTCGGTTGTGATG-G-AGCTGGT
1 TGAAGACACAAATCTTGCCTCTCTCGCTTGACA-GCGAAGCAGAT
5783441 TGAAGACA-ATAGATCTTGCCT-TC-CTGCATTGACAGCGAAGCAGAT
1 TGAAGACACA-A-ATCTTGCCTCTCTC-GC-TTGACAGCGAAGCAGAT
* * * * ** * *
5783486 CGAAGACACAAACCTTTCCTCTCTCGGTTGTGATG-G-AGCTGGT
1 TGAAGACACAAATCTTGCCTCTCTCGCTTGACA-GCGAAGCAGAT
* *** * *
5783529 TGAAGACAAAAGATCTTGCCT-TCCTATATTGATAGCGAAGCAGGT
1 TGAAGACACAA-ATCTTGCCTCT-CTCGCTTGACAGCGAAGCAGAT
** * * * * *
5783574 CCAAGACACAAACCTTGCCTCTCGGT-G-GTGA-TG-G-AGCTGGT
1 TGAAGACACAAATCTTGCCTCTC--TCGCTTGACAGCGAAGCAGAT
* * * * *
5783615 TGAAGACAAAAGATTTTGCCT-TC-CTG-TAATGACAGCGGAGCAAAC
1 TGAAGACACAA-ATCTTGCCTCTCTC-GCT--TGACAGCGAAGCAGAT
* * * *
5783660 TAAAGATAACAGATATTGCCT-TCCTACG-TTGACAGCGAAGCAGAT
1 TGAAGA-CACAAATCTTGCCTCT-CT-CGCTTGACAGCGAAGCAGAT
* * * ** * *
5783705 TGAAGACACAAACCTTGCCTCTCTCGGTTG-TAGTAAAGCTGGT
1 TGAAGACACAAATCTTGCCTCTCTCGCTTGACAGCGAAGCAGAT
* * *
5783748 TGAAGATAACAGATCTTGCCT-TCTTGCCTTGACAGCGAAGCAGAT
1 TGAAGA-CACAAATCTTGCCTCTCTCG-CTTGACAGCGAAGCAGAT
*
5783793 CGAAGACACAAATCTTGCCTCTCTCG
1 TGAAGACACAAATCTTGCCTCTCTCG
5783819 GTTACAGTGG
Statistics
Matches: 542, Mismatches: 152, Indels: 156
0.64 0.18 0.18
Matches are distributed among these distances:
40 1 0.00
41 16 0.03
42 30 0.06
43 125 0.23
44 194 0.36
45 160 0.30
46 13 0.02
47 2 0.00
48 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (44 bp):
TGAAGACACAAATCTTGCCTCTCTCGCTTGACAGCGAAGCAGAT
Found at i:5783839 original size:88 final size:88
Alignment explanation
Indices: 5783662--5783826 Score: 249
Period size: 88 Copynumber: 1.9 Consensus size: 88
5783652 GAGCAAACTA
* *
5783662 AAGATAACAGATATTGCCTTCCTACGTTGACAGCGAAGCAGATTGAAGACACAAACCTTGCCTCT
1 AAGATAACAGATATTGCCTTCCTACCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCT
** *
5783727 CTCGGTTGTAGTAAAGCTGGTTG
66 CTCGGTTACAGTAAAGCTGATTG
* * * *
5783750 AAGATAACAGATCTTGCCTTCTTGCCTTGACAGCGAAGCAGATCGAAGACACAAATCTTGCCTCT
1 AAGATAACAGATATTGCCTTCCTACCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCT
5783815 CTCGGTTACAGT
66 CTCGGTTACAGT
5783827 GGAACATATT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 69 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (88 bp):
AAGATAACAGATATTGCCTTCCTACCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCT
CTCGGTTACAGTAAAGCTGATTG
Found at i:5790969 original size:42 final size:42
Alignment explanation
Indices: 5790910--5790991 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
5790900 GTGTATCCTG
5790910 CAATTCCATGCCAATTACATGAATCGAAGTCTTTCCTTTTCC
1 CAATTCCATGCCAATTACATGAATCGAAGTCTTTCCTTTTCC
* *
5790952 CAATTCCATGCCAATTACATGAATGGAAGTCTTTTCTTTT
1 CAATTCCATGCCAATTACATGAATCGAAGTCTTTCCTTTT
5790992 ATTGGAAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (42 bp):
CAATTCCATGCCAATTACATGAATCGAAGTCTTTCCTTTTCC
Found at i:5799347 original size:28 final size:23
Alignment explanation
Indices: 5799323--5799369 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
5799313 TTTAATATAG
5799323 ATAT-TCTATTATTATATTACAA
1 ATATGTCTATTATTATATTACAA
5799345 ATATGTCTATTATTATATTACAA
1 ATATGTCTATTATTATATTACAA
5799368 AT
1 AT
5799370 TATAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATGTCTATTATTATATTACAA
Found at i:5804063 original size:21 final size:20
Alignment explanation
Indices: 5804013--5804063 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5804003 CCCATTTATT
*
5804013 TATTTTTTTTCTTTTTCAAC
1 TATTTTTTTTCATTTTCAAC
* * *
5804033 GATTTCTTTTCATTTTCACC
1 TATTTTTTTTCATTTTCAAC
5804053 TATTTTGTTTT
1 TATTTT-TTTT
5804064 TAAAAGTTAC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.14, C:0.16, G:0.04, T:0.67
Consensus pattern (20 bp):
TATTTTTTTTCATTTTCAAC
Found at i:5810964 original size:27 final size:27
Alignment explanation
Indices: 5810932--5810986 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
5810922 TAGTCTCTCC
* *
5810932 CAAAAAAATTAAAATAAATTTTAAAATT
1 CAAAATAATTAAAA-AAATTTCAAAATT
* *
5810960 CAAAATATTTATAAAAATTTCAAAATT
1 CAAAATAATTAAAAAAATTTCAAAATT
5810987 TATATTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (27 bp):
CAAAATAATTAAAAAAATTTCAAAATT
Found at i:5810974 original size:18 final size:19
Alignment explanation
Indices: 5810935--5810999 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
5810925 TCTCTCCCAA
5810935 AAAAATT-AAAATAAATTTT
1 AAAAATTCAAAAT-AATTTT
5810954 -AAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
5810972 AAAAATTTCAAAATTTATATTTT
1 AAAAA-TTCAAAA--TA-ATTTT
5810995 AAAAA
1 AAAAA
5811000 AGATAATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
17 4 0.11
18 7 0.18
19 9 0.24
20 7 0.18
22 1 0.03
23 6 0.16
24 4 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:5811180 original size:16 final size:16
Alignment explanation
Indices: 5811159--5811189 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5811149 TTTAAATTTT
5811159 TTTCAAATATACATGC
1 TTTCAAATATACATGC
*
5811175 TTTCAAATTTACATG
1 TTTCAAATATACATG
5811190 ATGTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (16 bp):
TTTCAAATATACATGC
Found at i:5815528 original size:16 final size:15
Alignment explanation
Indices: 5815482--5815533 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
5815472 AGAGTAAAAA
*
5815482 AGAAAATTGAAATGAT
1 AGAAAATT-AAAGGAT
* *
5815498 AGAAGATTTAAGGAT
1 AGAAAATTAAAGGAT
5815513 AGAAAATTAAAAGGAT
1 AGAAAATT-AAAGGAT
*
5815529 GGAAA
1 AGAAA
5815534 TCATAAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (15 bp):
AGAAAATTAAAGGAT
Found at i:5817136 original size:3 final size:3
Alignment explanation
Indices: 5817122--5817153 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5817112 TGTCGATGCC
*
5817122 GAT GAG GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
5817154 CGACGACGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:5817991 original size:13 final size:13
Alignment explanation
Indices: 5817973--5817997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5817963 AATAAATGGA
5817973 TATCGTTAAATTT
1 TATCGTTAAATTT
5817986 TATCGTTAAATT
1 TATCGTTAAATT
5817998 ATTACCTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TATCGTTAAATTT
Found at i:5818783 original size:10 final size:10
Alignment explanation
Indices: 5818642--5818832 Score: 50
Period size: 10 Copynumber: 19.3 Consensus size: 10
5818632 ATGAAAAACG
5818642 AAAATATT-T
1 AAAATATTAT
*
5818651 AAATTATTAT
1 AAAATATTAT
*
5818661 AAAAATTTTAGCT
1 -AAAATATTA--T
*
5818674 AAAA-GTTATT
1 AAAATATTA-T
5818684 AAAATATTATT
1 AAAATATTA-T
5818695 AAAA-A-T-T
1 AAAATATTAT
*
5818702 GAAA-ATTAT
1 AAAATATTAT
5818711 AGAAA-ATCTAT
1 A-AAATAT-TAT
*
5818722 CAAA-ATTAT
1 AAAATATTAT
* **
5818731 CAAATAACAT
1 AAAATATTAT
*
5818741 AAAAT-TTTT
1 AAAATATTAT
5818750 AAAA-ATATAT
1 AAAATAT-TAT
*
5818760 AAAA-ACTAT
1 AAAATATTAT
*
5818769 TAAATATTAT
1 AAAATATTAT
5818779 AAAATATTATT
1 AAAATATTA-T
* *
5818790 AATATGTTAT
1 AAAATATTAT
*
5818800 GAGAAA-A-T-G
1 -A-AAATATTAT
5818809 AAAATATTAAT
1 AAAATATT-AT
5818820 AAAATATTAT
1 AAAATATTAT
5818830 AAA
1 AAA
5818833 GAAATTAGAA
Statistics
Matches: 136, Mismatches: 26, Indels: 39
0.68 0.13 0.19
Matches are distributed among these distances:
7 8 0.06
8 3 0.02
9 29 0.21
10 50 0.37
11 39 0.29
12 6 0.04
13 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (10 bp):
AAAATATTAT
Found at i:5818891 original size:26 final size:27
Alignment explanation
Indices: 5818820--5818896 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 27
5818810 AAATATTAAT
5818820 AAAATATTATAAAGAAATTAGAAATGATAGA
1 AAAATA-TAT-AA-AAATTA-AAATGATAGA
*
5818851 AAATTATATCAAAAATTAAAATGATA-A
1 AAAATATAT-AAAAATTAAAATGATAGA
5818878 AAGAATATATAAAAATTAA
1 AA-AATATATAAAAATTAA
5818897 TAAAAAAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.29
28 14 0.33
29 6 0.14
30 5 0.12
31 5 0.12
ACGTcount: A:0.64, C:0.01, G:0.08, T:0.27
Consensus pattern (27 bp):
AAAATATATAAAAATTAAAATGATAGA
Found at i:5819427 original size:34 final size:34
Alignment explanation
Indices: 5819372--5819436 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
5819362 TTTACAAATT
5819372 ATTTTTAATAAAATAAATA-TTTTATTATTTTCCA
1 ATTTTTAATAAAATAAATATTTTTATT-TTTTCCA
**
5819406 ATTTTT-ATATAAATATTTATTTTTATTTTTT
1 ATTTTTAATA-AAATAAATATTTTTATTTTTT
5819437 AAAATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 3 0.11
34 17 0.63
35 7 0.26
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (34 bp):
ATTTTTAATAAAATAAATATTTTTATTTTTTCCA
Found at i:5821073 original size:23 final size:24
Alignment explanation
Indices: 5821047--5821097 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
5821037 GAGTCGAAAT
* *
5821047 TAAATTAT-TAATTTTTACAATAG
1 TAAATAATGTAATTTTTAAAATAG
*
5821070 TAAA-AATGTAATTTTTAAAATAT
1 TAAATAATGTAATTTTTAAAATAG
5821093 TAAAT
1 TAAAT
5821098 CAAAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (24 bp):
TAAATAATGTAATTTTTAAAATAG
Found at i:5821550 original size:17 final size:19
Alignment explanation
Indices: 5821530--5821572 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
5821520 CATTAAAAAA
5821530 ATAAACATA-TACT-AAAT
1 ATAAACATACTACTCAAAT
*
5821547 ATAAA-ATACTACTCTAAT
1 ATAAACATACTACTCAAAT
5821565 ATAAACAT
1 ATAAACAT
5821573 TAAATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 9 0.41
18 8 0.36
19 2 0.09
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAAACATACTACTCAAAT
Found at i:5823040 original size:29 final size:29
Alignment explanation
Indices: 5823006--5823061 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
5822996 TTAAAAAAGG
*
5823006 TTGAAACTAATACATTCTTGGCAAATTAT
1 TTGAAACTAATACATTCTTGACAAATTAT
*
5823035 TTGAAATTAATACATTCTTGACAAATT
1 TTGAAACTAATACATTCTTGACAAATT
5823062 TAACTTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (29 bp):
TTGAAACTAATACATTCTTGACAAATTAT
Found at i:5826015 original size:27 final size:25
Alignment explanation
Indices: 5825985--5826034 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
5825975 CACATAATCG
5825985 GGAAGCCCTCTCTTGAGCCAAATAACA
1 GGAAGCCCT-TC-TGAGCCAAATAACA
* *
5826012 GGAAGCTCTTCTGAGCCATATAA
1 GGAAGCCCTTCTGAGCCAAATAA
5826035 TGAGAAGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
26 2 0.10
27 8 0.38
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (25 bp):
GGAAGCCCTTCTGAGCCAAATAACA
Found at i:5826242 original size:26 final size:26
Alignment explanation
Indices: 5826172--5826243 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
5826162 AAGTTTAAGC
5826172 GAGCCATAT--CGGGAAGCTCACAAA
1 GAGCCATATAACGGGAAGCTCACAAA
* * *
5826196 GAGCC-TTTAATCAGGAAGCTCACGAA
1 GAGCCATATAA-CGGGAAGCTCACAAA
*
5826222 GAGCCATATAACGGGATGCTCA
1 GAGCCATATAACGGGAAGCTCA
5826244 TAAGAGCTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.05
24 5 0.13
26 27 0.71
27 4 0.11
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.17
Consensus pattern (26 bp):
GAGCCATATAACGGGAAGCTCACAAA
Found at i:5829860 original size:30 final size:31
Alignment explanation
Indices: 5829821--5829878 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
5829811 TTGTTGTTAT
*
5829821 TGTTTGTGTTCTGCAATTTGTT-TTTGTGTG
1 TGTTGGTGTTCTGCAATTTGTTGTTTGTGTG
* * *
5829851 TGTTGGTGTTTTGTATTTTGTTGTTTGT
1 TGTTGGTGTTCTGCAATTTGTTGTTTGT
5829879 TTTTATTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.05, C:0.03, G:0.28, T:0.64
Consensus pattern (31 bp):
TGTTGGTGTTCTGCAATTTGTTGTTTGTGTG
Found at i:5842428 original size:26 final size:26
Alignment explanation
Indices: 5842399--5842452 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
5842389 TCGAATAGTG
5842399 TATATACATATACATTATAAAATATA
1 TATATACATATACATTATAAAATATA
* * **
5842425 TATATATATTTGGATTATAAAATATA
1 TATATACATATACATTATAAAATATA
5842451 TA
1 TA
5842453 AAAACTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (26 bp):
TATATACATATACATTATAAAATATA
Found at i:5842645 original size:18 final size:18
Alignment explanation
Indices: 5842622--5842677 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
5842612 TATAGGTATA
*
5842622 ATAATAATAATATACAAT
1 ATAATAATAATATAAAAT
*
5842640 ATAATATTAATTAATAAAAT
1 ATAATAATAA-T-ATAAAAT
*
5842660 AAAATTAATAATATAAAA
1 ATAA-TAATAATATAAAA
5842678 ACAAAAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 9 0.29
19 7 0.23
20 10 0.32
21 5 0.16
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATAATAATATAAAAT
Found at i:5842667 original size:14 final size:14
Alignment explanation
Indices: 5842648--5842677 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5842638 ATATAATATT
5842648 AATTAATAAAATAA
1 AATTAATAAAATAA
*
5842662 AATTAATAATATAA
1 AATTAATAAAATAA
5842676 AA
1 AA
5842678 ACAAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATTAATAAAATAA
Found at i:5844058 original size:44 final size:44
Alignment explanation
Indices: 5843948--5844106 Score: 133
Period size: 44 Copynumber: 3.6 Consensus size: 44
5843938 CCGTCGTTAG
* * * *** *
5843948 TCTACTCCACTACTGCCTAGGGAGATAGAAT-TACTGGCTTCAA
1 TCTACTCCACTACTGCCCAGGGAGATAAAATCTGCAATCTTTAA
* * * * * *
5843991 TGTACTCCACT-GTAACCTCAGGGAGGTAAAATCTGCCATCTTTGA
1 TCTACTCCACTACT-GCC-CAGGGAGATAAAATCTGCAATCTTTAA
* * *
5844036 TCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTTAA
1 TCTACTCCACTACTGCCCAGGGAGATAAAATCTGCAATCTTTAA
*
5844080 TCTATTCCACTACTGCCCAGGGAGATA
1 TCTACTCCACTACTGCCCAGGGAGATA
5844107 GAATTACTGG
Statistics
Matches: 89, Mismatches: 23, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
42 1 0.01
43 12 0.13
44 57 0.64
45 18 0.20
46 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
TCTACTCCACTACTGCCCAGGGAGATAAAATCTGCAATCTTTAA
Found at i:5849139 original size:16 final size:15
Alignment explanation
Indices: 5849112--5849142 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5849102 CGCCTCTTTA
5849112 TAATTGAATGCCATG
1 TAATTGAATGCCATG
5849127 TAATTGTAATGCCATG
1 TAATTG-AATGCCATG
5849143 CAATCAGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (15 bp):
TAATTGAATGCCATG
Found at i:5850772 original size:18 final size:18
Alignment explanation
Indices: 5850749--5850804 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
5850739 TATAGGTATA
*
5850749 ATAATAATAATATACAAT
1 ATAATAATAATATAAAAT
*
5850767 ATAATATTAATTAATAAAAT
1 ATAATAATAA-T-ATAAAAT
*
5850787 AAAATTAATAATATAAAA
1 ATAA-TAATAATATAAAA
5850805 ACAAAAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 9 0.29
19 7 0.23
20 10 0.32
21 5 0.16
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATAATAATATAAAAT
Found at i:5850794 original size:14 final size:14
Alignment explanation
Indices: 5850775--5850804 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5850765 ATATAATATT
5850775 AATTAATAAAATAA
1 AATTAATAAAATAA
*
5850789 AATTAATAATATAA
1 AATTAATAAAATAA
5850803 AA
1 AA
5850805 ACAAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATTAATAAAATAA
Found at i:5856039 original size:16 final size:17
Alignment explanation
Indices: 5856007--5856039 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5855997 AATGTATTCT
*
5856007 AAATTACATATATATAA
1 AAATAACATATATATAA
5856024 AAATAACATA-ATATAA
1 AAATAACATATATATAA
5856040 GCCAGAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAACATATATATAA
Found at i:5862950 original size:83 final size:84
Alignment explanation
Indices: 5862805--5862960 Score: 208
Period size: 84 Copynumber: 1.9 Consensus size: 84
5862795 AGGGTTTTAA
* * * * * *
5862805 TTTTTTTGTAGTATTATTTATTTCTATGTTTGTCACTTAATTATAAAAAACTAAATAAATACTGA
1 TTTTTTTGTAGTATTATTTATCTCTATGCTTCTCAATTAAGTATAAAAAACTAAATAAATACTAA
5862870 AATGGTATATTTGAGAAGT
66 AATGGTATATTTGAGAAGT
* * *
5862889 TTTTTTTGTATTATTATTTATCTGTATGCTTCTTAATT-AGTATAAAAAAC-AAATTAAATACTA
1 TTTTTTTGTAGTATTATTTATCTCTATGCTTCTCAATTAAGTATAAAAAACTAAA-TAAATACTA
5862952 AAATGGTAT
65 AAATGGTAT
5862961 GGTTGAGGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
82 3 0.05
83 28 0.45
84 31 0.50
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (84 bp):
TTTTTTTGTAGTATTATTTATCTCTATGCTTCTCAATTAAGTATAAAAAACTAAATAAATACTAA
AATGGTATATTTGAGAAGT
Found at i:5862967 original size:83 final size:84
Alignment explanation
Indices: 5862805--5862967 Score: 204
Period size: 83 Copynumber: 2.0 Consensus size: 84
5862795 AGGGTTTTAA
* * * * * *
5862805 TTTTTTTGTAGTATTATTTATTTCTATGTTTGTCACTTAATTATAAAAAACTAAATAAATACTGA
1 TTTTTTTGTAGTATTATTTATCTCTATGCTTCTCAATTAAGTATAAAAAACTAAATAAATACTAA
*
5862870 AATGGTATATTTGAGAAGT
66 AATGGTATAGTTGAGAAGT
* * *
5862889 TTTTTTTGTATTATTATTTATCTGTATGCTTCTTAATT-AGTATAAAAAAC-AAATTAAATACTA
1 TTTTTTTGTAGTATTATTTATCTCTATGCTTCTCAATTAAGTATAAAAAACTAAA-TAAATACTA
*
5862952 AAATGGTATGGTTGAG
65 AAATGGTATAGTTGAG
5862968 GCGGGTTCTT
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
82 3 0.04
83 33 0.49
84 31 0.46
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (84 bp):
TTTTTTTGTAGTATTATTTATCTCTATGCTTCTCAATTAAGTATAAAAAACTAAATAAATACTAA
AATGGTATAGTTGAGAAGT
Found at i:5868650 original size:10 final size:12
Alignment explanation
Indices: 5868635--5868675 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 12
5868625 AGAATGAAAG
5868635 AACAAA-AA-AA
1 AACAAAGAACAA
5868645 AACAAAGAACAA
1 AACAAAGAACAA
5868657 AA-AAA-AACAA
1 AACAAAGAACAA
5868667 AACAAAGAA
1 AACAAAGAA
5868676 AATCCAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 13 0.48
11 8 0.30
12 6 0.22
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (12 bp):
AACAAAGAACAA
Found at i:5868677 original size:17 final size:17
Alignment explanation
Indices: 5868631--5868667 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
5868621 AGAAAGAATG
5868631 AAAGAACAAAAAAAAAC
1 AAAGAACAAAAAAAAAC
5868648 AAAGAACAAAAAAAAAC
1 AAAGAACAAAAAAAAAC
5868665 AAA
1 AAA
5868668 ACAAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (17 bp):
AAAGAACAAAAAAAAAC
Found at i:5868687 original size:17 final size:16
Alignment explanation
Indices: 5868632--5868687 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
5868622 GAAAGAATGA
*
5868632 AAGAACAAAAAAAAACA
1 AAGAAC-AAAAAAAACC
*
5868649 AAGAACAAAAAAAAAC
1 AAGAACAAAAAAAACC
*
5868665 AA-AACAAAGAAAATCC
1 AAGAACAAA-AAAAACC
5868681 AAGAACA
1 AAGAACA
5868688 GATCTAGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 6 0.18
16 17 0.52
17 10 0.30
ACGTcount: A:0.77, C:0.14, G:0.07, T:0.02
Consensus pattern (16 bp):
AAGAACAAAAAAAACC
Found at i:5870109 original size:26 final size:27
Alignment explanation
Indices: 5870058--5870109 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
5870048 TACTACAATC
*
5870058 ATTCAACAAAACACAAAAATTACTACA
1 ATTCAACAAAACAAAAAAATTACTACA
*
5870085 ATTCAAGAAAACAAAAAAATT-CTAC
1 ATTCAACAAAACAAAAAAATTACTAC
5870110 TGGTGCCGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.60, C:0.19, G:0.02, T:0.19
Consensus pattern (27 bp):
ATTCAACAAAACAAAAAAATTACTACA
Found at i:5870194 original size:31 final size:29
Alignment explanation
Indices: 5870106--5870195 Score: 74
Period size: 31 Copynumber: 2.9 Consensus size: 29
5870096 CAAAAAAATT
* * * *
5870106 CTACTGGTGCCGCCTAATAGTGCCCTTCCTT
1 CTACT-GTGCCGCTTGACAGTGCCC-TCCTC
5870137 CTACTGTGCCGCTTGACAGACT-CCCTCCTC
1 CTACTGTGCCGCTTGACAG--TGCCCTCCTC
*
5870167 CTATTGGTGCCGCTTGACATGTGCCCTCC
1 CTACT-GTGCCGCTTGACA-GTGCCCTCC
5870196 AACCTTGGTG
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
30 20 0.41
31 27 0.55
32 2 0.04
ACGTcount: A:0.12, C:0.38, G:0.20, T:0.30
Consensus pattern (29 bp):
CTACTGTGCCGCTTGACAGTGCCCTCCTC
Found at i:5875002 original size:25 final size:25
Alignment explanation
Indices: 5874957--5875079 Score: 119
Period size: 25 Copynumber: 5.0 Consensus size: 25
5874947 GTCATTCGGA
* *
5874957 TTACCGAT-TTCAGCTCTTATGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
* *
5874981 TTACCGATACTCAGCTCGTATGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
* *
5875006 TTACCGTTATTCAGCTTGGAAT-AGC
1 TTACCGTTATTCAGC-TCGTATGAGC
* * *
5875031 TTACTGTTATTCAGCTCGGAGGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
5875056 TTACCGTT-TAT-AGCTCGTATGAGC
1 TTACCGTTAT-TCAGCTCGTATGAGC
5875080 ATACATGTAC
Statistics
Matches: 82, Mismatches: 13, Indels: 8
0.80 0.13 0.08
Matches are distributed among these distances:
24 23 0.28
25 55 0.67
26 4 0.05
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (25 bp):
TTACCGTTATTCAGCTCGTATGAGC
Found at i:5875221 original size:26 final size:26
Alignment explanation
Indices: 5875190--5875241 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5875180 CACAGGTATT
5875190 TACATGAGATATATGA-AAATGATTTG
1 TACATGAGATATA-GATAAATGATTTG
* *
5875216 TACATGATATATAGATATATGATTTG
1 TACATGAGATATAGATAAATGATTTG
5875242 ATAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.38
Consensus pattern (26 bp):
TACATGAGATATAGATAAATGATTTG
Found at i:5878268 original size:50 final size:48
Alignment explanation
Indices: 5878209--5878344 Score: 211
Period size: 47 Copynumber: 2.8 Consensus size: 48
5878199 GGCAGTGAGT
* *
5878209 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGTTCGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAG--AGAGGA
* *
5878259 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TCGAGATGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGAGGA
5878306 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
5878345 CTGATATGTG
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
47 42 0.52
49 2 0.02
50 37 0.46
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.23
Consensus pattern (48 bp):
GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGAGGA
Found at i:5878326 original size:47 final size:47
Alignment explanation
Indices: 5878209--5878387 Score: 207
Period size: 47 Copynumber: 3.7 Consensus size: 47
5878199 GGCAGTGAGT
* * *
5878209 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGTTCGAGGA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TCG--AGATGA
*
5878259 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGA
* * * *
5878306 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTGATATGT
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTC-GAGATGA
* * *
5878354 GATCCCA-TGTAAGACCATATCTGGGATATGGCAT
1 G-TGCCAGTGTAAGACCATGTCTGGGACATGGCAT
5878388 TGGCAGTACA
Statistics
Matches: 116, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
47 43 0.37
48 31 0.27
49 5 0.04
50 37 0.32
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (47 bp):
GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGA
Found at i:5885197 original size:14 final size:14
Alignment explanation
Indices: 5885178--5885207 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5885168 AATTTGAATT
5885178 TTGAGTTAATCGAA
1 TTGAGTTAATCGAA
*
5885192 TTGAGTTATTCGAA
1 TTGAGTTAATCGAA
5885206 TT
1 TT
5885208 ATTCGAGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (14 bp):
TTGAGTTAATCGAA
Found at i:5885386 original size:20 final size:20
Alignment explanation
Indices: 5885347--5885408 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
5885337 TTCTCAACAA
5885347 AAATTACAAAATAGTTCAAAAT
1 AAATTACAAAA-A-TTCAAAAT
5885369 AAATTACAAAAATTCAAAAT
1 AAATTACAAAAATTCAAAAT
* *
5885389 -ATTTATAAAAATTCCAAAAT
1 AAATTACAAAAATT-CAAAAT
5885409 TTATATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.30
20 14 0.38
21 1 0.03
22 11 0.30
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (20 bp):
AAATTACAAAAATTCAAAAT
Found at i:5885410 original size:18 final size:19
Alignment explanation
Indices: 5885361--5885413 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
5885351 TACAAAATAG
* *
5885361 TTCAAAATAAATTACAAAAA
1 TTCAAAAT-ATTTATAAAAA
5885381 TTCAAAATATTTATAAAAA
1 TTCAAAATATTTATAAAAA
*
5885400 TTCCAAA-ATTTATA
1 TTCAAAATATTTATA
5885414 TTTTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 7 0.23
19 15 0.50
20 8 0.27
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (19 bp):
TTCAAAATATTTATAAAAA
Found at i:5897423 original size:26 final size:26
Alignment explanation
Indices: 5897387--5897439 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
5897377 GAATTCCTTA
5897387 AAGCTTTTCCCGATCTTGGGGACTTG
1 AAGCTTTTCCCGATCTTGGGGACTTG
*
5897413 AAGCTTTTCCCGATCTTGGGGATTTG
1 AAGCTTTTCCCGATCTTGGGGACTTG
5897439 A
1 A
5897440 TCTTCCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (26 bp):
AAGCTTTTCCCGATCTTGGGGACTTG
Found at i:5898020 original size:22 final size:21
Alignment explanation
Indices: 5897990--5898030 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5897980 GACAATTGGT
*
5897990 GCATGATTGGTTGTGAATTAA
1 GCATGATTGGATGTGAATTAA
*
5898011 GCATGAATTGGATGTTAATT
1 GCATG-ATTGGATGTGAATT
5898031 TACTTGTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.29, C:0.05, G:0.27, T:0.39
Consensus pattern (21 bp):
GCATGATTGGATGTGAATTAA
Found at i:5900553 original size:50 final size:50
Alignment explanation
Indices: 5900495--5900593 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
5900485 CGACCTACTT
* *
5900495 GATTTGCCCATGTAATAGCACACGCCCGTCTGCCCCCATATGGCCTAACC
1 GATTTGCCCATGTAATAGCACACGCCCGTCTGCCCCCACACGGCCTAACC
* * * * *
5900545 GATTTGCCCGTGTAATCGCACATGCTCGTGTGCCCCCACACGGCCTAAC
1 GATTTGCCCATGTAATAGCACACGCCCGTCTGCCCCCACACGGCCTAAC
5900594 ACACGGCCAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.22
Consensus pattern (50 bp):
GATTTGCCCATGTAATAGCACACGCCCGTCTGCCCCCACACGGCCTAACC
Found at i:5903844 original size:268 final size:268
Alignment explanation
Indices: 5903367--5904421 Score: 2013
Period size: 268 Copynumber: 3.9 Consensus size: 268
5903357 AAACCATTTC
*
5903367 ATTATTTTTAAAAAAACTTAAATAATTATTTAATCTTTGCAGTGGAAATTTCTAGAGTTTTAATT
1 ATTATTTTAAAAAAAACTTAAATAATTATTTAATCTTTGCAGTGGAAATTTCTAGAGTTTTAATT
5903432 TTGAAAATCAAATTTTTTGTAACACCCCTAACCCATATTCGTCACCGGAACAGGGTTACGAAGCA
66 TTGAAAATCAAATTTTTTGTAACACCCCTAACCCATATTCGTCACCGGAACAGGGTTACGAAGCA
*
5903497 TTACCAGAGTTTATAGATTAAATACGGTTATTCCATATCATTTACTATTCATATCAGAAATCAAT
131 TTACCAGAGTTTATAGATTAAATACAGTTATTCCATATCATTTACTATTCATATCAGAAATCAAT
5903562 CATATTCAATCATTATTGTCTTTTATATGAGACATCGAGGCCCAAAATATGCATTAATTTTGAAA
196 CATATTCAATCATTATTGTCTTTTATATGAGACATCGAGGCCCAAAATATGCATTAATTTTGAAA
5903627 ATTAAATA
261 ATTAAATA
5903635 ATTATTTTAAAAAAAACTTAAATAATTATTTAATCTTTGCAGTGGAAATTTCTAGAGTTTTAATT
1 ATTATTTTAAAAAAAACTTAAATAATTATTTAATCTTTGCAGTGGAAATTTCTAGAGTTTTAATT
* *
5903700 TTGAAAATCAAATTTTTTGTAACACCCCTAACCCATATTCATCACCTGAACAGGGTTACGAAGCA
66 TTGAAAATCAAATTTTTTGTAACACCCCTAACCCATATTCGTCACCGGAACAGGGTTACGAAGCA
5903765 TTACCAGAGTTTATAGATTAAATACAGTTATTCCATATCATTTACTATTCATATCAGAAATCAAT
131 TTACCAGAGTTTATAGATTAAATACAGTTATTCCATATCATTTACTATTCATATCAGAAATCAAT
*
5903830 CATATTCAATCATTATCGTCTTTTATATGAGACATCGAGGCCCAAAATATGCATTAATTTTGAAA
196 CATATTCAATCATTATTGTCTTTTATATGAGACATCGAGGCCCAAAATATGCATTAATTTTGAAA
5903895 ATTAAATA
261 ATTAAATA
*
5903903 ATTATTTAAAAAAAAACTTAAATAATTATTTAATCTTTGCAGTGGAAATTTCTAGAGTTTTAATT
1 ATTATTTTAAAAAAAACTTAAATAATTATTTAATCTTTGCAGTGGAAATTTCTAGAGTTTTAATT
*
5903968 TTGAAAATCAAAATTTTTGTAACACCCCTAACCCATATTCGTCACCGGAACAGGGTTACGAAGCA
66 TTGAAAATCAAATTTTTTGTAACACCCCTAACCCATATTCGTCACCGGAACAGGGTTACGAAGCA
5904033 TTACCAGAGTTTATAGATTAAATACAGTTATTCCATATCATTTACTATTCATATCAGAAATCAAT
131 TTACCAGAGTTTATAGATTAAATACAGTTATTCCATATCATTTACTATTCATATCAGAAATCAAT
*
5904098 CATATTCAATCATTATTGTCTTTTATATAAGACATCGAGGCCCAAAATATGCATTAATTTTGAAA
196 CATATTCAATCATTATTGTCTTTTATATGAGACATCGAGGCCCAAAATATGCATTAATTTTGAAA
5904163 ATTAAATA
261 ATTAAATA
5904171 ATTATTTT-AAAAAAACTTAAATAATTATTTAATCTTTGCAGTGGAAATTTCTAGAGTTTTAATT
1 ATTATTTTAAAAAAAACTTAAATAATTATTTAATCTTTGCAGTGGAAATTTCTAGAGTTTTAATT
5904235 TTGAAAATCAAATTTTTTTGTAACACCCCTAACCCATATTCGTCACCGGAACAGGGTTACGAAGC
66 TTGAAAATCAAA-TTTTTTGTAACACCCCTAACCCATATTCGTCACCGGAACAGGGTTACGAAGC
5904300 ATTACCAGAGTTTATAGATTAAATACAGTTATTCCATATCATTTACTATTCATATCAGAAATCAA
130 ATTACCAGAGTTTATAGATTAAATACAGTTATTCCATATCATTTACTATTCATATCAGAAATCAA
*
5904365 TCATATTCAATCATTATTGTCTTTTATATGAGACCTCGAGGCCCAAAATATGCATTA
195 TCATATTCAATCATTATTGTCTTTTATATGAGACATCGAGGCCCAAAATATGCATTA
5904422 GAAACAAGTC
Statistics
Matches: 771, Mismatches: 15, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
267 68 0.09
268 703 0.91
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (268 bp):
ATTATTTTAAAAAAAACTTAAATAATTATTTAATCTTTGCAGTGGAAATTTCTAGAGTTTTAATT
TTGAAAATCAAATTTTTTGTAACACCCCTAACCCATATTCGTCACCGGAACAGGGTTACGAAGCA
TTACCAGAGTTTATAGATTAAATACAGTTATTCCATATCATTTACTATTCATATCAGAAATCAAT
CATATTCAATCATTATTGTCTTTTATATGAGACATCGAGGCCCAAAATATGCATTAATTTTGAAA
ATTAAATA
Found at i:5905915 original size:26 final size:26
Alignment explanation
Indices: 5905878--5905935 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
5905868 GGAAGCTTTG
5905878 AAGAG-CTATTAATCAGGAAGCTCACA
1 AAGAGACTATTAATCAGGAAGCTC-CA
* *
5905904 AAGAGACT-TTAATCGGGAAGCTCCG
1 AAGAGACTATTAATCAGGAAGCTCCA
5905929 AAGAGAC
1 AAGAGAC
5905936 ATATATCAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 8 0.28
26 19 0.66
27 2 0.07
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (26 bp):
AAGAGACTATTAATCAGGAAGCTCCA
Found at i:5911542 original size:84 final size:84
Alignment explanation
Indices: 5911436--5911637 Score: 395
Period size: 84 Copynumber: 2.4 Consensus size: 84
5911426 TGTCTTCTGA
*
5911436 TCAACTTGCTAAGGAGGTGGAGGATAAATATTCTAGAATTGCTGCCTGGAAACCTTTTGTTGACA
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAATTGCTGCCTGGAAACCTTTTGTTGACA
5911501 AAACTCCCCAATCATCTTC
66 AAACTCCCCAATCATCTTC
5911520 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAATTGCTGCCTGGAAACCTTTTGTTGACA
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAATTGCTGCCTGGAAACCTTTTGTTGACA
5911585 AAACTCCCCAATCATCTTC
66 AAACTCCCCAATCATCTTC
5911604 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCT
1 TCAACTTGCTAAGGAGCTGGAGGATAAATATTCT
5911638 GCTCTATCTG
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 117 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (84 bp):
TCAACTTGCTAAGGAGCTGGAGGATAAATATTCTAGAATTGCTGCCTGGAAACCTTTTGTTGACA
AAACTCCCCAATCATCTTC
Found at i:5931099 original size:16 final size:18
Alignment explanation
Indices: 5931055--5931093 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5931045 TTATAATACT
5931055 TTATATTATATTATATTATG
1 TTATATT-TA-TATATTATG
*
5931075 TTATTTTTATATATTATG
1 TTATATTTATATATTATG
5931093 T
1 T
5931094 AATTTAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (18 bp):
TTATATTTATATATTATG
Found at i:5931221 original size:21 final size:20
Alignment explanation
Indices: 5931175--5931245 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 20
5931165 TGTTAAGATG
* *
5931175 ATTATATAAAAAATTTAATA
1 ATTAAATAAAAAATTAAATA
* *
5931195 AATAAATAAAAATATTAAATT
1 ATTAAATAAAAA-ATTAAATA
*
5931216 ATTAAATATTAAAA-TAATATA
1 ATTAAATA-AAAAATTAA-ATA
5931237 ATATAAATA
1 AT-TAAATA
5931246 TTTTTTTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
20 13 0.32
21 18 0.45
22 9 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTAAATAAAAAATTAAATA
Found at i:5935855 original size:24 final size:24
Alignment explanation
Indices: 5935809--5935856 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5935799 GTATAAAATA
5935809 CCAAATTTTATAAATCATATTTGT
1 CCAAATTTTATAAATCATATTTGT
5935833 CCAAA-TTTATACAAT-ATAGTTTGT
1 CCAAATTTTATA-AATCATA-TTTGT
5935857 GTAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (24 bp):
CCAAATTTTATAAATCATATTTGT
Found at i:5936507 original size:11 final size:11
Alignment explanation
Indices: 5936493--5936517 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5936483 TTTTTTTAAA
5936493 TTTAAAAGATT
1 TTTAAAAGATT
5936504 TTTAAAAGATT
1 TTTAAAAGATT
5936515 TTT
1 TTT
5936518 TTTATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (11 bp):
TTTAAAAGATT
Found at i:5936557 original size:12 final size:11
Alignment explanation
Indices: 5936530--5936570 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
5936520 TATTTTTTAA
5936530 TTTTAAAATAT
1 TTTTAAAATAT
5936541 TTTTAAAATAT
1 TTTTAAAATAT
*
5936552 TTTT-TAA-AT
1 TTTTAAAATAT
5936561 TTTTAAAATA
1 TTTTAAAATA
5936571 GATTTTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 6 0.23
10 4 0.15
11 16 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:5936563 original size:38 final size:38
Alignment explanation
Indices: 5936472--5936569 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 38
5936462 TAAATATATT
5936472 TATTTTTTAAATTTTTTTAAATTTAAAAGATTTTTAAAA
1 TATTTTTTAAA-TTTTTTAAATTTAAAAGATTTTTAAAA
* ** * *
5936511 GATTTTTTTTATTTTTTAATTTTAAAATATTTTTAAAA
1 TATTTTTTAAATTTTTTAAATTTAAAAGATTTTTAAAA
*
5936549 TATTTTTTAAATTTTTAAAAT
1 TATTTTTTAAATTTTTTAAAT
5936570 AGATTTTTTG
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
38 41 0.84
39 8 0.16
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (38 bp):
TATTTTTTAAATTTTTTAAATTTAAAAGATTTTTAAAA
Found at i:5936576 original size:20 final size:20
Alignment explanation
Indices: 5936539--5936576 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5936529 ATTTTAAAAT
**
5936539 ATTTTTAAAATATTTTTTAA
1 ATTTTTAAAATAGATTTTAA
5936559 ATTTTTAAAATAGATTTT
1 ATTTTTAAAATAGATTTT
5936577 TTGGTATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
ATTTTTAAAATAGATTTTAA
Found at i:5938329 original size:17 final size:18
Alignment explanation
Indices: 5938304--5938341 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5938294 TTTAGTTTCA
*
5938304 TTTATTTTTCA-AATAAT
1 TTTAATTTTCATAATAAT
*
5938321 TTTAATTTTCATAATACT
1 TTTAATTTTCATAATAAT
5938339 TTT
1 TTT
5938342 TAAGCTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAATTTTCATAATAAT
Found at i:5938429 original size:16 final size:17
Alignment explanation
Indices: 5938395--5938429 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5938385 TTTTGGACTG
5938395 TATTGGACCTATCTAATA
1 TATTGGACCTA-CTAATA
5938413 TATTGGACCTA-TAATA
1 TATTGGACCTACTAATA
5938429 T
1 T
5938430 TTTATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
18 11 0.65
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (17 bp):
TATTGGACCTACTAATA
Found at i:5943064 original size:145 final size:145
Alignment explanation
Indices: 5942801--5943095 Score: 554
Period size: 145 Copynumber: 2.0 Consensus size: 145
5942791 TTTTTCAAAG
5942801 ATATTGTTGAAGAAGGTGATCTTGTTTGTCATTTGCAGCCATGGAAGCTTTATGTTGTTGCTTTC
1 ATATTGTTGAAGAAGGTGATCTTGTTTGTCATTTGCAGCCATGGAAGCTTTATGTTGTTGCTTTC
*
5942866 TCTTTGGATGACTGCTGCAACTACAACCCCTCTGTGATATGATTCTGGGCTGAGATCCTGCATCA
66 TCTTTGGATGACTGCCGCAACTACAACCCCTCTGTGATATGATTCTGGGCTGAGATCCTGCATCA
*
5942931 GCAATAACTTATATT
131 GCAATAACTGATATT
5942946 ATATTGTTGAAGAAGGTGATCTTGTTTGTCATTTGCAGCCATGGAAGCTTTATGTTGTTGCTTTC
1 ATATTGTTGAAGAAGGTGATCTTGTTTGTCATTTGCAGCCATGGAAGCTTTATGTTGTTGCTTTC
* *
5943011 TCTTTGGATGAGTGCCGCAACTACAACCCCTCTGTGATATGATTCTGGGCTGAGATGCTGCATCA
66 TCTTTGGATGACTGCCGCAACTACAACCCCTCTGTGATATGATTCTGGGCTGAGATCCTGCATCA
5943076 GCAATAACTGATATT
131 GCAATAACTGATATT
5943091 ATATT
1 ATATT
5943096 ATATATTATG
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
145 146 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (145 bp):
ATATTGTTGAAGAAGGTGATCTTGTTTGTCATTTGCAGCCATGGAAGCTTTATGTTGTTGCTTTC
TCTTTGGATGACTGCCGCAACTACAACCCCTCTGTGATATGATTCTGGGCTGAGATCCTGCATCA
GCAATAACTGATATT
Found at i:5948874 original size:14 final size:14
Alignment explanation
Indices: 5948852--5948884 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
5948842 TTTATTTTAC
5948852 AAATA-ATTTTTTT
1 AAATATATTTTTTT
5948865 AAATATATTTTTTT
1 AAATATATTTTTTT
5948879 -AATATA
1 AAATATA
5948885 CTCTTATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AAATATATTTTTTT
Found at i:5951972 original size:18 final size:18
Alignment explanation
Indices: 5951949--5951989 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
5951939 ATAGGTTTTA
5951949 AATTAAATAATTTT-AATT
1 AATTAAA-AATTTTAAATT
5951967 AATTAAAAATTTTAAATT
1 AATTAAAAATTTTAAATT
5951985 AATTA
1 AATTA
5951990 CACCTTGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTAAAAATTTTAAATT
Found at i:5951984 original size:14 final size:15
Alignment explanation
Indices: 5951944--5951986 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 15
5951934 CTAGAATAGG
5951944 TTTTAAATTAAATAA
1 TTTTAAATTAAATAA
5951959 TTTTAATTAATTAAA-AA
1 TTTT-A--AATTAAATAA
5951976 TTTTAAATTAA
1 TTTTAAATTAA
5951987 TTACACCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 6 0.24
15 4 0.16
16 2 0.08
17 6 0.24
18 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAAATTAAATAA
Found at i:5966148 original size:21 final size:21
Alignment explanation
Indices: 5966110--5966173 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
5966100 TACCTACGCC
*
5966110 ATACTAGAGAGCACCGTAGTGCT
1 ATAC-AGAG-GCATCGTAGTGCT
5966133 ATACAGAGGCATCGTAGTGCT
1 ATACAGAGGCATCGTAGTGCT
*
5966154 ATACAGAGGCATCATAGTGC
1 ATACAGAGGCATCGTAGTGC
5966174 AAACAAAAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 31 0.79
22 4 0.10
23 4 0.10
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
ATACAGAGGCATCGTAGTGCT
Found at i:5972079 original size:19 final size:19
Alignment explanation
Indices: 5972049--5972123 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
5972039 GGATTATGTG
*
5972049 CTTGTGTGCCA-GTATGCA
1 CTTGTGTACCAGGTATGCA
**
5972067 CTTCGTGTACCAGGTATGTG
1 CTT-GTGTACCAGGTATGCA
* *
5972087 CTTATGCACCA-GTATGCA
1 CTTGTGTACCAGGTATGCA
*
5972105 CTTTGTGTGCCAGGTATGC
1 C-TTGTGTACCAGGTATGC
5972124 GTTTTATATG
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
18 9 0.21
19 20 0.47
20 14 0.33
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (19 bp):
CTTGTGTACCAGGTATGCA
Found at i:5972085 original size:38 final size:38
Alignment explanation
Indices: 5972043--5972122 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
5972033 AGTATGGGAT
* **
5972043 TATGTGCTTGTGTGCCAGTATGCACTTCGTGTACCAGG
1 TATGTGCTTATGCACCAGTATGCACTTCGTGTACCAGG
* *
5972081 TATGTGCTTATGCACCAGTATGCACTTTGTGTGCCAGG
1 TATGTGCTTATGCACCAGTATGCACTTCGTGTACCAGG
5972119 TATG
1 TATG
5972123 CGTTTTATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.35
Consensus pattern (38 bp):
TATGTGCTTATGCACCAGTATGCACTTCGTGTACCAGG
Found at i:5976595 original size:57 final size:58
Alignment explanation
Indices: 5976532--5976649 Score: 166
Period size: 57 Copynumber: 2.1 Consensus size: 58
5976522 CTTTTTCAAG
* * * * *
5976532 TCATTTTCATTTTGGAGAAAACTACATTCATTTCCAATTGATTCC-ATTTCTCCATTT
1 TCATTTTCATTTAGGAGAAAACCACAATAATTTCCAAATGATTCCTATTTCTCCATTT
* *
5976589 TCATTTTCATTTAGGAGAAAACCATAATAATTTCCAAATGTTTCCTATTTCTCCATTT
1 TCATTTTCATTTAGGAGAAAACCACAATAATTTCCAAATGATTCCTATTTCTCCATTT
5976647 TCA
1 TCA
5976650 CCATTTATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 38 0.72
58 15 0.28
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (58 bp):
TCATTTTCATTTAGGAGAAAACCACAATAATTTCCAAATGATTCCTATTTCTCCATTT
Found at i:5981235 original size:27 final size:27
Alignment explanation
Indices: 5981203--5981371 Score: 187
Period size: 27 Copynumber: 6.3 Consensus size: 27
5981193 CCTAAAATAG
* *
5981203 GGTAAAATAATCGAAATACCCCCATAA
1 GGTAAAATGACCGAAATACCCCCATAA
* * *
5981230 GATAAAATGACCGAAATAGCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAA
* * **
5981257 GGTAAAATAACCAAAATACCTTCAT-A
1 GGTAAAATGACCGAAATACCCCCATAA
*
5981283 GAGTAAAATGACCGAAATAACCCCATAA
1 G-GTAAAATGACCGAAATACCCCCATAA
* *
5981311 GGTAAAATGACCGGAATACCCCCATAT
1 GGTAAAATGACCGAAATACCCCCATAA
* * *
5981338 GGTAAAATGACTGAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAA
5981365 GGTAAAA
1 GGTAAAA
5981372 CGATTGTTAT
Statistics
Matches: 116, Mismatches: 24, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
26 1 0.01
27 113 0.97
28 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCCCATAA
Found at i:5981290 original size:54 final size:53
Alignment explanation
Indices: 5981199--5981371 Score: 215
Period size: 54 Copynumber: 3.2 Consensus size: 53
5981189 AGACCCTAAA
*
5981199 ATAGGGTAAAATAATCGAAATACCCCCATA-AGATAAAATGACCGAAATAGCCCC
1 ATAGGGTAAAATAACCGAAATACCCCCATAGAG-TAAAATGACCGAAATA-CCCC
* **
5981253 ATAGGGTAAAATAACCAAAATACCTTCATAGAGTAAAATGACCGAAATAACCCC
1 ATAGGGTAAAATAACCGAAATACCCCCATAGAGTAAAATGACCGAAAT-ACCCC
* * * *
5981307 ATAAGGTAAAATGACCGGAATACCCCCATATG-GTAAAATGACTGAAATACCCTC
1 ATAGGGTAAAATAACCGAAATACCCCCATA-GAGTAAAATGACCGAAATACCC-C
5981361 ATAGGGTAAAA
1 ATAGGGTAAAA
5981372 CGATTGTTAT
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
53 4 0.04
54 95 0.92
55 4 0.04
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (53 bp):
ATAGGGTAAAATAACCGAAATACCCCCATAGAGTAAAATGACCGAAATACCCC
Found at i:5981342 original size:81 final size:81
Alignment explanation
Indices: 5981199--5981371 Score: 238
Period size: 81 Copynumber: 2.1 Consensus size: 81
5981189 AGACCCTAAA
* * *
5981199 ATAGGGTAAAATAATCGAAATACCCCCATAAGATAAAATGACCGAAATAGCCCCATAGGGTAAAA
1 ATAGGGTAAAATAACCGAAATAACCCCATAAGATAAAATGACCGAAATACCCCCATAGGGTAAAA
*
5981264 TAACCAAAATACCTTC
66 TAACCAAAATACCCTC
* * * * *
5981280 ATAGAGTAAAATGACCGAAATAACCCCATAAGGTAAAATGACCGGAATACCCCCATATGGTAAAA
1 ATAGGGTAAAATAACCGAAATAACCCCATAAGATAAAATGACCGAAATACCCCCATAGGGTAAAA
* **
5981345 TGACTGAAATACCCTC
66 TAACCAAAATACCCTC
5981361 ATAGGGTAAAA
1 ATAGGGTAAAA
5981372 CGATTGTTAT
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (81 bp):
ATAGGGTAAAATAACCGAAATAACCCCATAAGATAAAATGACCGAAATACCCCCATAGGGTAAAA
TAACCAAAATACCCTC
Found at i:5981447 original size:25 final size:26
Alignment explanation
Indices: 5981390--5981454 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
5981380 ATACTCCTAC
*
5981390 GATATGAAATGACTGTTATGGCTTTAT
1 GATATG-AATGACTGTTATGGCTCTAT
*
5981417 GTTATGAATGACTGATT-T-GCTCTAT
1 GATATGAATGACTG-TTATGGCTCTAT
*
5981442 GATATGTATGACT
1 GATATGAATGACT
5981455 ATGATTGAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 17 0.52
26 9 0.27
27 7 0.21
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.42
Consensus pattern (26 bp):
GATATGAATGACTGTTATGGCTCTAT
Found at i:5982813 original size:17 final size:18
Alignment explanation
Indices: 5982793--5982827 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5982783 CTTAAATTAG
5982793 GGAAAACTG-AAACTGTA
1 GGAAAACTGAAAACTGTA
5982810 GGAAAACTGAAAACTGTA
1 GGAAAACTGAAAACTGTA
5982828 CGAAGACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.49, C:0.11, G:0.23, T:0.17
Consensus pattern (18 bp):
GGAAAACTGAAAACTGTA
Found at i:5989440 original size:26 final size:26
Alignment explanation
Indices: 5989411--5989468 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
5989401 CTGAACAAAT
* * *
5989411 TTTTGGCGATTTTACCCCTGGTAAAA
1 TTTTGACGAATTTACCCCTAGTAAAA
* *
5989437 TTTTGACGAATTTGCCCTTAGTAAAA
1 TTTTGACGAATTTACCCCTAGTAAAA
5989463 TTTTGA
1 TTTTGA
5989469 GAAAATATGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (26 bp):
TTTTGACGAATTTACCCCTAGTAAAA
Found at i:5992260 original size:13 final size:13
Alignment explanation
Indices: 5992242--5992266 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5992232 AATTTAATAA
5992242 AAAAACACTAGGT
1 AAAAACACTAGGT
5992255 AAAAACACTAGG
1 AAAAACACTAGG
5992267 GGTTTGTCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.16, T:0.12
Consensus pattern (13 bp):
AAAAACACTAGGT
Found at i:5996555 original size:20 final size:21
Alignment explanation
Indices: 5996522--5996565 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
5996512 GTAGACAGAA
*
5996522 AAACCTCGTTTTAATAT-ATC
1 AAACCTCGTTTTAAAATGATC
5996542 AAACCTC-TTATTAAAATGATC
1 AAACCTCGTT-TTAAAATGATC
5996563 AAA
1 AAA
5996566 TTACGAGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 13 0.62
21 6 0.29
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (21 bp):
AAACCTCGTTTTAAAATGATC
Found at i:6000503 original size:23 final size:23
Alignment explanation
Indices: 6000452--6000504 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
6000442 AGTGTTATTG
6000452 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
6000475 -TACAGTGGTAG-TTACGGCTACAT
1 AT-CAGTGGTAGCTT-CGGCTACAT
6000498 ATCAGTG
1 ATCAGTG
6000505 TGGCACTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 3 0.11
23 23 0.85
24 1 0.04
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:6003325 original size:15 final size:15
Alignment explanation
Indices: 6003305--6003334 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6003295 ATTTTTGTAT
*
6003305 TATTTTAATATTAAA
1 TATTTTAAAATTAAA
6003320 TATTTTAAAATTAAA
1 TATTTTAAAATTAAA
6003335 AAATATATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTTAAAATTAAA
Found at i:6011370 original size:105 final size:105
Alignment explanation
Indices: 6011128--6011393 Score: 318
Period size: 115 Copynumber: 2.4 Consensus size: 105
6011118 AACTAATAAT
* * *
6011128 TAATTTATAATAGTTACTAACAAAATAACTTTCAAATAAATTAAAAATATTAAAAGATTACATTC
1 TAATTTATAATAGTTACTAACAAAATAACTTTAAAATAAATTAAAAATAATAAAAAATTACATTC
* **
6011193 ATAATCTAACAAACCACAATAAACCTTAAACCCTAAACAAA
66 ATAACCTAACAAACCACAATAAACAGTAAA-CCTAAACAAA
* * * *
6011234 CAATTAACCTAACCACAAAACTTACTAACAAAATAACTTTAAAATAAATTAAAAATTAATAAAAA
1 TAATT----T----ATAATAGTTACTAACAAAATAACTTTAAAATAAATTAAAAA-TAATAAAAA
*
6011299 ATTACATTCATAACCTAACAAATCACAATAAACAGTAAA-CTAAACAAA
57 ATTACATTCATAACCTAACAAACCACAATAAACAGTAAACCTAAACAAA
* *
6011347 TAATTTATAATAGTAACTGACAAAATAACTTTAAAATAAATTAAAAA
1 TAATTTATAATAGTTACTAACAAAATAACTTTAAAATAAATTAAAAA
6011394 CAACATAAAA
Statistics
Matches: 134, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
105 36 0.27
106 4 0.03
109 1 0.01
110 1 0.01
113 13 0.10
114 37 0.28
115 42 0.31
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.27
Consensus pattern (105 bp):
TAATTTATAATAGTTACTAACAAAATAACTTTAAAATAAATTAAAAATAATAAAAAATTACATTC
ATAACCTAACAAACCACAATAAACAGTAAACCTAAACAAA
Found at i:6011544 original size:22 final size:22
Alignment explanation
Indices: 6011504--6011556 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
6011494 ATCCTTGTTT
* *
6011504 TTTCTTCTCCTTTCTTTCTTTC
1 TTTCTTCTCCTCTCTTTCTTCC
6011526 TTTCTTCTCC-CTCTCTTCTTCC
1 TTTCTTCTCCTCTCT-TTCTTCC
6011548 TTCTCTTCT
1 TT-TCTTCT
6011557 GCTATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 18 0.67
23 6 0.22
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTCTTCTCCTCTCTTTCTTCC
Found at i:6011554 original size:12 final size:11
Alignment explanation
Indices: 6011504--6011556 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
6011494 ATCCTTGTTT
6011504 TTTCTTC-TCC
1 TTTCTTCTTCC
*
6011514 TTTCTTTCTTTC
1 TTTC-TTCTTCC
*
6011526 TTTCTTCTCCC
1 TTTCTTCTTCC
*
6011537 TCTCTTCTTCC
1 TTTCTTCTTCC
6011548 TTCTCTTCT
1 TT-TCTTCT
6011557 GCTATTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 4 0.12
11 18 0.53
12 12 0.35
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTCTTCTTCC
Found at i:6011697 original size:27 final size:27
Alignment explanation
Indices: 6011633--6011691 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
6011623 ATTGGTACCC
*
6011633 CCTATCAGATAGGGGTCACTGGTGCCA
1 CCTATAAGATAGGGGTCACTGGTGCCA
6011660 CCTATAAGATAGGGGTCACTGGTGCCA
1 CCTATAAGATAGGGGTCACTGGTGCCA
6011687 CCTAT
1 CCTAT
6011692 TGGATAAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (27 bp):
CCTATAAGATAGGGGTCACTGGTGCCA
Found at i:6011925 original size:29 final size:29
Alignment explanation
Indices: 6011883--6011939 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
6011873 GGCACCACCA
*
6011883 CTATTGACATACCATTGTCGTATTTAATC
1 CTATTGACATACCATTGTCATATTTAATC
*
6011912 CTATTGACATACCATTTTCATATTTAAT
1 CTATTGACATACCATTGTCATATTTAAT
6011940 TTTTTTTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (29 bp):
CTATTGACATACCATTGTCATATTTAATC
Found at i:6016737 original size:31 final size:29
Alignment explanation
Indices: 6016699--6016775 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
6016689 ATTAATGCTC
*
6016699 AGTGACTAAAATGTTACAACACAATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* ***
6016730 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
6016759 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
6016776 CTGAGACAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 1 0.03
31 17 0.43
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:6017716 original size:12 final size:12
Alignment explanation
Indices: 6017699--6017740 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 12
6017689 TTTTCCCCAT
6017699 AAAAATATTATA
1 AAAAATATTATA
6017711 AAAAATAAAATTATA
1 AAAAAT---ATTATA
6017726 AAAAATATT-TA
1 AAAAATATTATA
6017737 AAAA
1 AAAA
6017741 TATGAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 6 0.22
12 9 0.33
15 12 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAAATATTATA
Found at i:6017730 original size:10 final size:10
Alignment explanation
Indices: 6017717--6017895 Score: 65
Period size: 10 Copynumber: 18.3 Consensus size: 10
6017707 TATAAAAAAT
6017717 AAAATTATAA
1 AAAATTATAA
*
6017727 AAAA-TATTTA
1 AAAATTA-TAA
*
6017737 AAAA-TAT-G
1 AAAATTATAA
*
6017745 AAAATTGATAC
1 AAAATT-ATAA
*
6017756 AAATTTAT-A
1 AAAATTATAA
* *
6017765 AATATTATTA
1 AAAATTATAA
6017775 AAAATTAT-A
1 AAAATTATAA
*
6017784 AATATTATAA
1 AAAATTATAA
* *
6017794 TAAA-TCTAA
1 AAAATTATAA
* *
6017803 CAAATTCTAAA
1 AAAATTAT-AA
6017814 AAAATTAT--
1 AAAATTATAA
6017822 AAAATTAATAA
1 AAAATT-ATAA
6017833 AAATATT-TAA
1 AAA-ATTATAA
**
6017843 AATTTTATAA
1 AAAATTATAA
*
6017853 AAACA-TAT-T
1 AAA-ATTATAA
*
6017862 AAAATTCTATA
1 AAAATTATA-A
*
6017873 AAAATCATAA
1 AAAATTATAA
*
6017883 AAATTTATAA
1 AAAATTATAA
6017893 AAA
1 AAA
6017896 GTATTAAAAT
Statistics
Matches: 126, Mismatches: 26, Indels: 34
0.68 0.14 0.18
Matches are distributed among these distances:
8 11 0.09
9 34 0.27
10 55 0.44
11 23 0.18
12 3 0.02
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (10 bp):
AAAATTATAA
Found at i:6017732 original size:27 final size:29
Alignment explanation
Indices: 6017697--6017825 Score: 87
Period size: 28 Copynumber: 4.6 Consensus size: 29
6017687 TATTTTCCCC
6017697 ATAAAAATATTATAAAAA-AT-AAAATT-
1 ATAAAAATATTATAAAAATATGAAAATTG
6017723 ATAAAAAATATT-TAAAAATATGAAAATTG
1 AT-AAAAATATTATAAAAATATGAAAATTG
* * *
6017752 ATACAAAT-TTATAAATATTATTAAAAATT-
1 ATAAAAATATTATAAA-AATA-TGAAAATTG
* *
6017781 AT--AAATATTATAATAAATCTAACAAATT-
1 ATAAAAATATTATAA-AAATATGA-AAATTG
* *
6017809 CTAAAAAAATTATAAAA
1 ATAAAAATATTATAAAA
6017826 TTAATAAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
26 8 0.10
27 20 0.24
28 29 0.35
29 10 0.12
30 17 0.20
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (29 bp):
ATAAAAATATTATAAAAATATGAAAATTG
Found at i:6017833 original size:20 final size:20
Alignment explanation
Indices: 6017810--6017895 Score: 72
Period size: 20 Copynumber: 4.3 Consensus size: 20
6017800 TAACAAATTC
*
6017810 TAAAAAAATTATAAAATTAA
1 TAAAAAAATTATAAAATTTA
*
6017830 TAAAAATATT-TAAAATTTTA
1 TAAAAAAATTATAAAA-TTTA
*
6017850 TAAAAACA-TATTAAAATTCTA
1 TAAAAAAATTA-TAAAATT-TA
*
6017871 T--AAAAATCATAAAAATTTA
1 TAAAAAAATTAT-AAAATTTA
6017890 TAAAAA
1 TAAAAA
6017896 GTATTAAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
19 14 0.26
20 28 0.53
21 11 0.21
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAAAATTATAAAATTTA
Found at i:6017855 original size:21 final size:20
Alignment explanation
Indices: 6017810--6017919 Score: 93
Period size: 21 Copynumber: 5.5 Consensus size: 20
6017800 TAACAAATTC
* *
6017810 TAAAAAA-ATTATAAAATTAA
1 TAAAAAATATTA-AAATTTTA
6017830 T-AAAAATATTTAAAATTTTA
1 TAAAAAATA-TTAAAATTTTA
*
6017850 TAAAAACATATTAAAATTCTA
1 TAAAAA-ATATTAAAATTTTA
*
6017871 T-AAAAATCA-TAAAAATTTA
1 TAAAAAAT-ATTAAAATTTTA
* *
6017890 TAAAAAGTATTAAAATTGATA
1 TAAAAAATATTAAAATT-TTA
6017911 TAAAAAATA
1 TAAAAAATA
6017920 AAAATCATAA
Statistics
Matches: 73, Mismatches: 9, Indels: 15
0.75 0.09 0.15
Matches are distributed among these distances:
19 17 0.23
20 25 0.34
21 28 0.38
22 3 0.04
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (20 bp):
TAAAAAATATTAAAATTTTA
Found at i:6017903 original size:20 final size:19
Alignment explanation
Indices: 6017697--6017924 Score: 106
Period size: 19 Copynumber: 11.9 Consensus size: 19
6017687 TATTTTCCCC
*
6017697 ATAAAAATATTATAAAA--A
1 ATAAAAATATTA-AAAATTT
* *
6017715 ATAAAATTATAAAAAATATT
1 ATAAAAATATTAAAAAT-TT
* *
6017735 -TAAAAATA-TGAAAATTG
1 ATAAAAATATTAAAAATTT
* *
6017752 ATACAAAT-TTATAAATATT
1 ATAAAAATATTAAAAAT-TT
* *
6017771 ATTAAAA-ATTATAAATATT
1 ATAAAAATATTAAAAAT-TT
*
6017790 ATAATAAAT-CTAACAAATTCT
1 ATAA-AAATATTAA-AAATT-T
*
6017811 A-AAAAA-ATTATAAAATTA
1 ATAAAAATATTA-AAAATTT
*
6017829 ATAAAAATATTTAAAATTTT
1 ATAAAAATA-TTAAAAATTT
6017849 ATAAAAACATATT-AAAATTCT
1 AT-AAAA-ATATTAAAAATT-T
6017870 ATAAAAATCA-TAAAAATTT
1 ATAAAAAT-ATTAAAAATTT
6017889 ATAAAAAGTATT-AAAATTGAT
1 ATAAAAA-TATTAAAAATT--T
6017910 ATAAAAA-A-TAAAAAT
1 ATAAAAATATTAAAAAT
6017925 CATAAAAACT
Statistics
Matches: 163, Mismatches: 21, Indels: 51
0.69 0.09 0.22
Matches are distributed among these distances:
17 5 0.03
18 28 0.17
19 66 0.40
20 35 0.21
21 26 0.16
22 3 0.02
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAAAAATATTAAAAATTT
Found at i:6018336 original size:29 final size:28
Alignment explanation
Indices: 6018304--6018359 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
6018294 CGTTTTTATC
* * *
6018304 AATTTTAATATTTTTTTATTATTTTTAAG
1 AATTATAATATGTTTTT-TTAATTTTAAG
6018333 AATTATAATATGTTTTTTTAATTTTAA
1 AATTATAATATGTTTTTTTAATTTTAA
6018360 ATATGTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (28 bp):
AATTATAATATGTTTTTTTAATTTTAAG
Found at i:6018369 original size:49 final size:47
Alignment explanation
Indices: 6018268--6018378 Score: 120
Period size: 49 Copynumber: 2.3 Consensus size: 47
6018258 TCCAATTCAA
*
6018268 GTTTTTATGATTTTTAAATATTTATACGTTTTTATCAATTTTAATAT
1 GTTTTTATTATTTTTAAATATTTATACGTTTTTATCAATTTTAATAT
* * *
6018315 TTTTTTATTATTTTTAAGA-ATTATAATATGTTTTT-TTAATTTTAAATAT
1 GTTTTTATTATTTTTAA-ATATT-T-ATACGTTTTTATCAATTTT-AATAT
*
6018364 GTTTTT-TTAATTTTA
1 GTTTTTATTATTTTTA
6018379 TAATTTTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
47 18 0.33
48 17 0.31
49 19 0.35
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (47 bp):
GTTTTTATTATTTTTAAATATTTATACGTTTTTATCAATTTTAATAT
Found at i:6018387 original size:19 final size:21
Alignment explanation
Indices: 6018335--6018395 Score: 92
Period size: 20 Copynumber: 3.0 Consensus size: 21
6018325 TTTTTAAGAA
6018335 TTATAATATGTTTTTTTAATT
1 TTATAATATGTTTTTTTAATT
6018356 TTA-AATATGTTTTTTTAATT
1 TTATAATATGTTTTTTTAATT
*
6018376 TTATAAT-T-TTTTTGTAATT
1 TTATAATATGTTTTTTTAATT
6018395 T
1 T
6018396 ATTTCAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
19 11 0.29
20 21 0.55
21 6 0.16
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
TTATAATATGTTTTTTTAATT
Found at i:6018446 original size:10 final size:9
Alignment explanation
Indices: 6018269--6018451 Score: 52
Period size: 10 Copynumber: 19.4 Consensus size: 9
6018259 CCAATTCAAG
*
6018269 TTTTTATGA
1 TTTTTATAA
6018278 TTTTTA-AA
1 TTTTTATAA
* *
6018286 TATTTATACG
1 TTTTTATA-A
6018296 TTTTTATCAA
1 TTTTTAT-AA
* *
6018306 TTTTAATATT
1 TTTTTATA-A
*
6018316 TTTTTATTA
1 TTTTTATAA
*
6018325 TTTTTAAGAA
1 TTTTT-ATAA
* * *
6018335 TTATAATATG
1 TTTTTATA-A
*
6018345 TTTTTTTAA
1 TTTTTATAA
* *
6018354 TTTTAAATATG
1 TTTT-TATA-A
*
6018365 TTTTTTTAA
1 TTTTTATAA
6018374 -TTTTATAA
1 TTTTTATAA
*
6018382 TTTTTTTGTAA
1 --TTTTTATAA
6018393 TTTATT-TCAA
1 TTT-TTAT-AA
*
6018403 TTTATTA-GA
1 TTT-TTATAA
*
6018412 TTTCTAT-A
1 TTTTTATAA
6018420 TTTTTATAA
1 TTTTTATAA
*
6018429 TATTTATAA
1 TTTTTATAA
6018438 GTTTTTATAA
1 -TTTTTATAA
6018448 TTTT
1 TTTT
6018452 ATAGCAATAT
Statistics
Matches: 124, Mismatches: 33, Indels: 34
0.65 0.17 0.18
Matches are distributed among these distances:
8 22 0.18
9 40 0.32
10 50 0.40
11 12 0.10
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:6018475 original size:9 final size:9
Alignment explanation
Indices: 6018461--6018528 Score: 50
Period size: 10 Copynumber: 7.3 Consensus size: 9
6018451 TATAGCAATA
6018461 TTAATATTT
1 TTAATATTT
*
6018470 TTAATACTT
1 TTAATATTT
*
6018479 TTAGT-TTT
1 TTAATATTT
6018487 TATAATATTTT
1 T-TAATA-TTT
6018498 TTAA-ATTT
1 TTAATATTT
**
6018506 TTCTTGATTT
1 TTAAT-ATTT
6018516 TTAATCATTT
1 TTAAT-ATTT
6018526 TTA
1 TTA
6018529 TAGGAAATTA
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
8 8 0.18
9 16 0.36
10 17 0.38
11 4 0.09
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (9 bp):
TTAATATTT
Found at i:6018909 original size:24 final size:25
Alignment explanation
Indices: 6018881--6018929 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
6018871 TTATATTATT
*
6018881 ATTTTGAAAT-AAAAAATATATAAA
1 ATTTTAAAATCAAAAAATATATAAA
* *
6018905 ATTTTAAAATCATAAGATATATAAA
1 ATTTTAAAATCAAAAAATATATAAA
6018930 TTAATAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
ATTTTAAAATCAAAAAATATATAAA
Found at i:6019083 original size:17 final size:16
Alignment explanation
Indices: 6019057--6019094 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
6019047 TATATGTTTA
6019057 TATATTTTTATAAATT
1 TATATTTTTATAAATT
*
6019073 TATAGTTTTTATTAATT
1 TATA-TTTTTATAAATT
6019090 TATAT
1 TATAT
6019095 ATTATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TATATTTTTATAAATT
Found at i:6027505 original size:2 final size:2
Alignment explanation
Indices: 6027498--6027528 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6027488 TTTCCGTCTA
6027498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6027529 ACCTTTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6031409 original size:17 final size:17
Alignment explanation
Indices: 6031387--6031421 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6031377 ATTTAAAAGT
6031387 ATTTAGTT-AGTATTTGA
1 ATTTAGTTGA-TATTTGA
6031404 ATTTAGTTGATATTTGA
1 ATTTAGTTGATATTTGA
6031421 A
1 A
6031422 CTTTTATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.51
Consensus pattern (17 bp):
ATTTAGTTGATATTTGA
Found at i:6031565 original size:12 final size:12
Alignment explanation
Indices: 6031543--6031585 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
6031533 TGTGGTGGAC
6031543 ATAAA-TTAAAA
1 ATAAATTTAAAA
6031554 ATAAATTTAAAA
1 ATAAATTTAAAA
* *
6031566 AAAAATTTAAAT
1 ATAAATTTAAAA
6031578 ATAAATTT
1 ATAAATTT
6031586 TTAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 5 0.18
12 23 0.82
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAAATTTAAAA
Found at i:6031595 original size:16 final size:17
Alignment explanation
Indices: 6031574--6031608 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
6031564 AAAAAAATTT
6031574 AAATATAAATTTTT-AA
1 AAATATAAATTTTTGAA
6031590 AAATATAAATTTTTGAA
1 AAATATAAATTTTTGAA
6031607 AA
1 AA
6031609 GTTCAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
AAATATAAATTTTTGAA
Done.